Individual skill
ontology-term-resolution
Resolve free-text scientific labels to ontology term IDs and validate existing CURIEs against the EBI Ontology Lookup Service (OLS4). Also look up prefixes in Bioregistry, resolve compact identifiers via Identifiers.org, map lab shorthand with ZOOMA, and build Ontobee term pages. Use whenever an ontology identifier must be produced or checked - annotating tissue, cell type, disease, phenotype, assay, chemical, organism, sex, or developmental stage fields; preparing metadata for GEO, ENA, BioSamples, CELLxGENE, HCA, or ISA-Tab submission; auditing a metadata table of term IDs; checking whether a term is obsolete and what replaced it; or deciding HPO vs HP. Triggers include "ontology term", "ontology ID", "CURIE", "controlled vocabulary", "UBERON", "CL:", "MONDO", "HPO", "EFO", "ChEBI", "NCBITaxon", "GO term", "PATO", "Zooma", "Bioregistry", "Identifiers.org", "Ontobee", "annotate this tissue/cell type/disease", and any request to emit or verify an identifier shaped like PREFIX:0001234.
plugins/KalarisLabs/research-agent-skills/skills/ontology-term-resolution/SKILL.md
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- Last checked
- Nov 4, 2026
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- 1,532
- Repository last updated
- Nov 6, 2026
- License
- Apache-2.0
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- ontologies,-curies,-ols,-metadata-annotation,-fair-data Declared skill tag
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SKILL.mdcore · 12,705 bytesSKILL.mdcore · 12,705 bytesSKILL.mdcore · 12,705 bytesSKILL.mdcore · 12,705 bytesSKILL.mdcore · 12,705 bytesSKILL.mdcore · 12,705 bytesSKILL.mdcore · 12,705 bytesSKILL.mdcore · 12,705 bytesSKILL.mdcore · 12,705 bytesSKILL.mdcore · 12,705 bytesSKILL.mdcore · 12,705 bytesSKILL.mdcore · 12,705 bytesSKILL.mdcore · 12,705 bytesreferences/companion-apis.mddoc · 7,624 bytesreferences/curation-rules.mddoc · 5,511 bytesreferences/ols4-api.mddoc · 6,117 bytesreferences/ontology-registry.mddoc · 5,617 bytesscripts/id_client.pyruns · 11,816 bytesscripts/lookup_prefix.pyruns · 6,669 bytesscripts/map_terms.pyruns · 7,582 bytesscripts/ols_client.pyruns · 12,456 bytesscripts/resolve_terms.pyruns · 8,160 bytesscripts/validate_terms.pyruns · 9,746 bytesscripts/zooma_client.pyruns · 4,621 bytes
Read excerpt
# Ontology Term Resolution
## When to use
Any time an ontology identifier is about to be written down or trusted: annotating a metadata
column, filling a submission template, auditing a table someone else produced, or checking whether
an ID in an old file is still current.
## The rule
**Never write an ontology ID from memory, and never accept one without checking it.**
Ontology IDs are memorable in form and arbitrary in detail. A plausible-looking `UBERON:0002108`
is a real term (small intestine) that is not the liver, and nothing downstream will catch the